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I think you misunderstood his point. He noted that Islam is not inherently intolerant, citing historical examples of Christians and Jews who were free to confess their faith under Muslim rule. Pelikan's point was that we need to be careful about how we advance arguments in favor of tolerance. If we argue for tolerance because "no one can really be sure he is right", we will alienate committed believers of any tradition. Pelikan's point, using the example of "Dignitatis Humanae", is that there is a more effective argument for tolerance, rooted in the firm belief in the inherent dignity of every person created by God.